3moo: Difference between revisions

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-[[Image:3moo.png|left|200px]]
-{{STRUCTURE_3moo|  PDB=3moo  |  SCENE=  }}
+==Crystal structure of the HmuO, heme oxygenase from Corynebacterium diphtheriae, in complex with azide-bound verdoheme==
+<StructureSection load='3moo' size='340' side='right'caption='[[3moo]], [[Resolution|resolution]] 1.71&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3moo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MOO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MOO FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.71&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=VEA:5-OXA-PROTOPORPHYRIN+IX+CONTAINING+FE'>VEA</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3moo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3moo OCA], [https://pdbe.org/3moo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3moo RCSB], [https://www.ebi.ac.uk/pdbsum/3moo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3moo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q54AI1_CORDP Q54AI1_CORDP]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The least understood mechanism during heme degradation by the enzyme heme oxygenase (HO) is the third step of ring opening of verdoheme to biliverdin, a process which maintains iron homeostasis. In response to this mechanistic uncertainty, we launched a combined study of X-ray crystallography and theoretical QM/MM calculations, designed to elucidate the mechanism. The air-sensitive ferrous verdoheme complex of HmuO, a heme oxygenase from Corynebacterium diphtheriae, was crystallized under anaerobic conditions. Spectral analysis of the azide-bound verdoheme-HmuO complex crystals assures that the verdoheme group remains intact during the crystallization and X-ray diffraction measurement. The structure offers the first solid evidence for the presence of a water cluster in the distal pocket of this catalytically critical intermediate. The subsequent QM/MM calculations based on this crystal structure explore the reaction mechanisms starting from the FeOOH-verdoheme and FeHOOH-verdoheme complexes, which mimic, respectively, the O(2)- and H(2)O(2)-supported degradations. In both mechanisms, the rate-determining step is the initial O-O bond breaking step, which is either homolytic (for FeHOOH-verdoheme) or coupled to electron and proton transfers (in FeOOH-verdoheme). Additionally, the calculations indicate that the FeHOOH-verdoheme complex is more reactive than the FeOOH-verdoheme complex in accord with experimental findings. QM energies with embedded MM charges are close to and yield the same conclusions as full QM/MM energies. Finally, the calculations highlight the dominant influence of the distal water cluster which acts as a biocatalyst for the conversion of verdoheme to biliverdin in the two processes, by fixing the departing OH and directing it to the requisite site of attack, and by acting as a proton shuttle and a haven for the highly reactive OH(-) nucleophile.
-===Crystal structure of the HmuO, heme oxygenase from Corynebacterium diphtheriae, in complex with azide-bound verdoheme===
+Enzymatic ring-opening mechanism of verdoheme by the heme oxygenase: a combined X-ray crystallography and QM/MM study.,Lai W, Chen H, Matsui T, Omori K, Unno M, Ikeda-Saito M, Shaik S J Am Chem Soc. 2010 Sep 22;132(37):12960-70. PMID:20806922<ref>PMID:20806922</ref>
-{{ABSTRACT_PUBMED_20806922}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3moo" style="background-color:#fffaf0;"></div>
-[[3moo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_diphtheriae Corynebacterium diphtheriae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MOO OCA].
 ==See Also==
-*[[Heme oxygenase|Heme oxygenase]]
+*[[Heme oxygenase 3D structures|Heme oxygenase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020806922</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Corynebacterium diphtheriae]]
-[[Category: Ikeda-Saito, M.]]
+[[Category: Large Structures]]
-[[Category: Matsui, T.]]
+[[Category: Ikeda-Saito M]]
-[[Category: Omori, K.]]
+[[Category: Matsui T]]
-[[Category: Unno, M.]]
+[[Category: Omori K]]
-[[Category: Absorption spectra]]
+[[Category: Unno M]]
-[[Category: Anaerobic chamber]]
-[[Category: Ferrous verdoheme]]
-[[Category: Heme oxygenase]]
-[[Category: Oxidoreductase]]
-[[Category: Reaction intermediate]]
-[[Category: Reaction mechanism]]